I just realised there's some other clear evidence as well:
If all the dialogues you just typed about the Force bonds was regarding Kreia (One of you would have to die) the Exile would have died on Malachor, since the bond he shares with Kreia is made that way. But he doesn't, assuming it was him flying the Ebon Hawk towards the Unknow Regions at the end-game.
PS: Kreia's body remains when killed!

If all those dialogues were about Nihilus, it would mean the Exile would have to die at the bridge of the Ravager. Instead, he picks up the tainted mask, and actually becomes stronger in the Force!. This supports the theory that he is actually 'bonded' with himself, hence, he doesn't die. And when Nihilus goes up in a cloud of Dark Energy, the Exile becomes stronger. Note: You can't change your alignment from this point. Does this mean the Exile is 'whole' again now Nihilus is dead?

Hmm..this theory might be woth a shot..maybe post it on Obsidian Forums? Very good thread!